membrane-annotator 0.1.0

Generate membrane segmentations from vesicle and double membrane masks

Segmentation process

This runs locally membrane creation. Given some previous annotations on copick (that correspond to either double membranes or filled out objects), we create membrane annotations which we save to copick.

Usage: python change_layers.py --run-id 19032 --session-id NAME_OF_ID_WITH_ANNOTATIONS Note: An object annotation should paint the entire object, where the membrane is constructed by considering the outer border. A membrane annotation corresponds to a double membrane, where the double membrane is processed by splitting into two.

Example (from two object annotations):

Further notes

The copick config visicle_config_increment.json should be used for the nninteractive-launch --config. Each object (double membrane or entire blob that we should extract a border from) should correspond to one label. A single membrane (i.e requires no processing) should be labeled with label class type "single".